diff --git a/scripts/agent-branch-finish.sh b/scripts/agent-branch-finish.sh
index d63539c..104ef8f 100755
--- a/scripts/agent-branch-finish.sh
+++ b/scripts/agent-branch-finish.sh
@@ -227,7 +227,68 @@ if [[ "$SOURCE_BRANCH" == "$BASE_BRANCH" ]]; then
   exit 1
 fi
 
+cleanup_missing_merged_source_branch() {
+  local state_line=""
+  local parsed_state=""
+  local parsed_merged_at=""
+  local parsed_url=""
+  local remote_delete_output=""
+  local prune_args=()
+
+  if [[ "$MERGE_MODE" != "pr" || "$CLEANUP_AFTER_MERGE" -ne 1 ]]; then
+    return 1
+  fi
+  if ! command -v "$GH_BIN" >/dev/null 2>&1; then
+    return 1
+  fi
+
+  state_line="$("$GH_BIN" pr list \
+    --state merged \
+    --head "$SOURCE_BRANCH" \
+    --base "$BASE_BRANCH" \
+    --json state,mergedAt,url \
+    --jq 'sort_by(.mergedAt // "") | reverse | (.[0] // {}) | [(.state // ""), (.mergedAt // ""), (.url // "")] | join("\u001f")' \
+    2>/dev/null || true)"
+  if [[ -z "$state_line" ]]; then
+    return 1
+  fi
+
+  IFS=$'\x1f' read -r parsed_state parsed_merged_at parsed_url <<< "$state_line"
+  if [[ "$parsed_state" != "MERGED" && -z "$parsed_merged_at" ]]; then
+    return 1
+  fi
+
+  echo "[agent-branch-finish] Local source branch '${SOURCE_BRANCH}' is already absent, but a merged PR exists; continuing cleanup." >&2
+  if [[ -n "$parsed_url" ]]; then
+    echo "[agent-branch-finish] Merged PR: ${parsed_url}" >&2
+  fi
+
+  run_guardex_cli locks release --branch "$SOURCE_BRANCH" >/dev/null 2>&1 || true
+
+  if [[ "$PUSH_ENABLED" -eq 1 && "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+    if git -C "$repo_root" ls-remote --exit-code --heads origin "$SOURCE_BRANCH" >/dev/null 2>&1; then
+      if ! remote_delete_output="$(git -C "$repo_root" push origin --delete "$SOURCE_BRANCH" 2>&1)"; then
+        echo "[agent-branch-finish] Warning: remote branch cleanup failed for '${SOURCE_BRANCH}'." >&2
+        [[ -n "$remote_delete_output" ]] && echo "$remote_delete_output" >&2
+      fi
+    fi
+  fi
+
+  prune_args=(worktree prune --base "$BASE_BRANCH" --only-dirty-worktrees --delete-branches)
+  if [[ "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+    prune_args+=(--delete-remote-branches)
+  fi
+  if ! run_guardex_cli "${prune_args[@]}"; then
+    echo "[agent-branch-finish] Warning: automatic worktree prune failed." >&2
+    echo "[agent-branch-finish] You can run manual cleanup: gx cleanup --base ${BASE_BRANCH}" >&2
+  fi
+
+  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via pr flow and found source branch/worktree already cleaned."
+  exit 0
+}
+
 if ! git -C "$repo_root" show-ref --verify --quiet "refs/heads/${SOURCE_BRANCH}"; then
+  cleanup_missing_merged_source_branch
   echo "[agent-branch-finish] Local source branch does not exist: ${SOURCE_BRANCH}" >&2
   exit 1
 fi
diff --git a/templates/scripts/agent-branch-finish.sh b/templates/scripts/agent-branch-finish.sh
index d63539c..104ef8f 100755
--- a/templates/scripts/agent-branch-finish.sh
+++ b/templates/scripts/agent-branch-finish.sh
@@ -227,7 +227,68 @@ if [[ "$SOURCE_BRANCH" == "$BASE_BRANCH" ]]; then
   exit 1
 fi
 
+cleanup_missing_merged_source_branch() {
+  local state_line=""
+  local parsed_state=""
+  local parsed_merged_at=""
+  local parsed_url=""
+  local remote_delete_output=""
+  local prune_args=()
+
+  if [[ "$MERGE_MODE" != "pr" || "$CLEANUP_AFTER_MERGE" -ne 1 ]]; then
+    return 1
+  fi
+  if ! command -v "$GH_BIN" >/dev/null 2>&1; then
+    return 1
+  fi
+
+  state_line="$("$GH_BIN" pr list \
+    --state merged \
+    --head "$SOURCE_BRANCH" \
+    --base "$BASE_BRANCH" \
+    --json state,mergedAt,url \
+    --jq 'sort_by(.mergedAt // "") | reverse | (.[0] // {}) | [(.state // ""), (.mergedAt // ""), (.url // "")] | join("\u001f")' \
+    2>/dev/null || true)"
+  if [[ -z "$state_line" ]]; then
+    return 1
+  fi
+
+  IFS=$'\x1f' read -r parsed_state parsed_merged_at parsed_url <<< "$state_line"
+  if [[ "$parsed_state" != "MERGED" && -z "$parsed_merged_at" ]]; then
+    return 1
+  fi
+
+  echo "[agent-branch-finish] Local source branch '${SOURCE_BRANCH}' is already absent, but a merged PR exists; continuing cleanup." >&2
+  if [[ -n "$parsed_url" ]]; then
+    echo "[agent-branch-finish] Merged PR: ${parsed_url}" >&2
+  fi
+
+  run_guardex_cli locks release --branch "$SOURCE_BRANCH" >/dev/null 2>&1 || true
+
+  if [[ "$PUSH_ENABLED" -eq 1 && "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+    if git -C "$repo_root" ls-remote --exit-code --heads origin "$SOURCE_BRANCH" >/dev/null 2>&1; then
+      if ! remote_delete_output="$(git -C "$repo_root" push origin --delete "$SOURCE_BRANCH" 2>&1)"; then
+        echo "[agent-branch-finish] Warning: remote branch cleanup failed for '${SOURCE_BRANCH}'." >&2
+        [[ -n "$remote_delete_output" ]] && echo "$remote_delete_output" >&2
+      fi
+    fi
+  fi
+
+  prune_args=(worktree prune --base "$BASE_BRANCH" --only-dirty-worktrees --delete-branches)
+  if [[ "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+    prune_args+=(--delete-remote-branches)
+  fi
+  if ! run_guardex_cli "${prune_args[@]}"; then
+    echo "[agent-branch-finish] Warning: automatic worktree prune failed." >&2
+    echo "[agent-branch-finish] You can run manual cleanup: gx cleanup --base ${BASE_BRANCH}" >&2
+  fi
+
+  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via pr flow and found source branch/worktree already cleaned."
+  exit 0
+}
+
 if ! git -C "$repo_root" show-ref --verify --quiet "refs/heads/${SOURCE_BRANCH}"; then
+  cleanup_missing_merged_source_branch
   echo "[agent-branch-finish] Local source branch does not exist: ${SOURCE_BRANCH}" >&2
   exit 1
 fi
diff --git a/test/finish.test.js b/test/finish.test.js
index 0691c30..be40a3d 100644
--- a/test/finish.test.js
+++ b/test/finish.test.js
@@ -698,6 +698,71 @@ exit 1
   assert.equal(result.stdout.trim(), '', 'agent branch should be deleted on origin');
 });
 
+test('agent-branch-finish cleanup is idempotent after merged PR already pruned branch and worktree', () => {
+  const repoDir = initRepo();
+  seedCommit(repoDir);
+  attachOriginRemote(repoDir);
+
+  let result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['add', '.'], repoDir);
+  assert.equal(result.status, 0, result.stderr);
+  result = runCmd('git', ['commit', '-m', 'apply gx setup'], repoDir, {
+    ALLOW_COMMIT_ON_PROTECTED_BRANCH: '1',
+  });
+  assert.equal(result.status, 0, result.stderr);
+  result = runCmd('git', ['push', 'origin', 'dev'], repoDir);
+  assert.equal(result.status, 0, result.stderr);
+
+  result = runCmd('git', ['checkout', '-b', 'agent/test-pr-already-cleaned'], repoDir);
+  assert.equal(result.status, 0, result.stderr);
+  commitFile(repoDir, 'already-cleaned.txt', 'already cleaned\n', 'already cleaned change');
+  result = runCmd('git', ['push', '-u', 'origin', 'agent/test-pr-already-cleaned'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['checkout', 'dev'], repoDir);
+  assert.equal(result.status, 0, result.stderr);
+  result = runCmd('git', ['branch', '-D', 'agent/test-pr-already-cleaned'], repoDir);
+  assert.equal(result.status, 0, result.stderr);
+  result = runCmd('git', ['push', 'origin', '--delete', 'agent/test-pr-already-cleaned'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const { fakePath: fakeGhPath } = createFakeGhScript(`
+if [[ "$1" == "pr" && "$2" == "list" ]]; then
+  if [[ " $* " == *" --state merged "* ]] && [[ " $* " == *" --head agent/test-pr-already-cleaned "* ]] && [[ " $* " == *" --base dev "* ]]; then
+    printf 'MERGED\\x1f2026-04-25T11:03:00Z\\x1fhttps://example.test/pr/already-cleaned\\n'
+    exit 0
+  fi
+  echo "unexpected gh pr list args: $*" >&2
+  exit 1
+fi
+if [[ "$1" == "pr" && ( "$2" == "create" || "$2" == "merge" || "$2" == "view" ) ]]; then
+  echo "already-cleaned rerun should not call gh pr $2" >&2
+  exit 1
+fi
+echo "unexpected gh args: $*" >&2
+exit 1
+`);
+
+  const finish = runBranchFinish(
+    ['--branch', 'agent/test-pr-already-cleaned', '--base', 'dev', '--mode', 'pr', '--cleanup'],
+    repoDir,
+    { GUARDEX_GH_BIN: fakeGhPath },
+  );
+  assert.equal(finish.status, 0, finish.stderr || finish.stdout);
+  assert.match(
+    finish.stderr,
+    /Local source branch 'agent\/test-pr-already-cleaned' is already absent, but a merged PR exists; continuing cleanup\./,
+  );
+  assert.match(
+    finish.stderr,
+    /Merged PR: https:\/\/example\.test\/pr\/already-cleaned/,
+  );
+  assert.match(
+    finish.stdout,
+    /Merged 'agent\/test-pr-already-cleaned' into 'dev' via pr flow and found source branch\/worktree already cleaned\./,
+  );
+});
+
 
 test('agent-branch-finish cleanup succeeds from active agent worktree when base branch is checked out elsewhere', () => {
   const repoDir = initRepo();